Contacts of the helix formed by residues 1394 - 1402 (chain A) in PDB entry 4YOC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035A TYR 3.5 15.3 - - - -
1363A ARG* 5.3 0.9 - - - -
1368A ARG 5.2 0.4 - - - -
1369A ASP* 2.9 40.0 + - - -
1372A SER* 5.5 0.7 - - - -
1392A PRO 3.4 1.2 + - - -
1393A GLN* 1.3 82.7 - - - +
1395A TRP* 1.3 60.3 + - - +
1396A PHE 3.6 2.3 + - - -
1397A GLN* 3.1 20.2 + - - +
1398A ARG* 2.9 40.2 + - - +
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Residues in contact with TRP1395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035A TYR 4.4 2.0 + - - -
1036A HIS 4.2 1.4 + - - -
1037A ALA 3.8 17.3 - - - +
1038A ASP* 3.4 29.4 - - + -
1039A ILE* 3.5 53.4 - - + +
1040A ASN* 4.7 2.8 + - - -
1073A GLN* 4.0 10.5 - - - +
1076A SER* 6.1 0.2 - - - -
1077A MET* 5.3 6.2 - - - -
1305A GLY* 5.3 2.9 - - - -
1332A HIS* 4.8 6.5 - + - -
1363A ARG* 5.5 4.3 - - - +
1365A ILE* 4.5 9.9 - - + -
1394A SER* 1.3 73.1 - - - +
1396A PHE* 1.3 91.6 + + + +
1398A ARG* 3.1 20.7 + - - +
1399A GLN* 2.9 73.5 + - + +
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Residues in contact with PHE1396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305A GLY 3.0 28.9 - - - -
1306A VAL* 4.5 9.0 - - + -
1363A ARG* 6.1 0.4 - - - +
1365A ILE* 4.0 13.9 - - + -
1369A ASP* 3.5 32.3 - - + +
1370A THR* 3.7 25.4 - - + -
1394A SER* 3.3 2.2 + - - +
1395A TRP* 1.3 100.8 - + + +
1397A GLN* 1.3 58.2 + - - +
1399A GLN* 3.0 5.9 + - + +
1400A LEU* 2.9 56.4 + - + +
1555A ARG* 3.4 27.1 - - - -
1558A GLY* 4.3 7.6 - - - -
1583A PRO* 5.7 1.8 - - + -
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Residues in contact with GLN1397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368A ARG 3.3 2.4 + - - -
1369A ASP 3.2 17.6 + - - +
1370A THR 4.3 0.7 - - - +
1371A MET 4.1 0.6 - - - +
1372A SER* 2.9 40.4 + - - +
1373A ASP* 3.2 33.4 + - - +
1392A PRO* 4.1 7.9 - - + -
1393A GLN* 2.6 35.2 + - - -
1394A SER* 3.1 19.2 + - - +
1396A PHE* 1.3 76.7 - - + +
1398A ARG* 1.3 57.7 + - - +
1400A LEU* 3.7 5.3 - - - +
1401A ARG* 2.9 36.7 + - - +
1555A ARG* 3.9 10.5 - - - +
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Residues in contact with ARG1398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A HIS* 2.2 56.1 + - - -
1038A ASP* 2.3 32.5 + - - +
1073A GLN* 6.1 0.4 - - - -
1392A PRO* 4.0 25.9 + - + +
1394A SER* 2.9 13.4 + - - +
1395A TRP* 3.1 38.5 + - - +
1397A GLN* 1.3 75.0 - - - +
1399A GLN* 1.3 63.7 + - - +
1402A GLY* 3.0 32.9 + - - +
866C GLN* 6.2 2.0 - - - +
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Residues in contact with GLN1399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A GLN* 3.9 15.3 + - - +
1077A MET* 3.6 33.3 - - - +
1395A TRP* 2.9 66.9 + - + +
1396A PHE* 3.4 7.2 - - + +
1398A ARG* 1.3 83.7 - - - +
1400A LEU* 1.3 69.2 + - + +
1401A ARG 3.5 0.7 + - - -
1402A GLY* 3.8 6.4 + - - -
1560A PRO* 5.8 0.9 - - - +
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Residues in contact with LEU1400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396A PHE* 2.9 56.2 + - + +
1397A GLN* 4.2 2.7 - - - +
1399A GLN* 1.3 85.6 - - + +
1401A ARG* 1.3 59.8 + - - +
1555A ARG* 3.6 24.7 - - - +
1558A GLY* 4.1 15.3 - - - +
1559A PHE 3.3 27.6 - - - +
1560A PRO* 3.8 11.0 - - + +
1561A ASP* 2.9 37.3 + - - +
1562A THR* 4.7 1.4 + - - +
1583A PRO* 6.3 0.7 - - + -
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Residues in contact with ARG1401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373A ASP* 2.8 34.9 + - - +
1388A TYR* 3.4 42.6 - - + +
1390A GLY 2.9 24.9 + - - -
1391A GLU 3.7 4.8 + - - -
1392A PRO* 3.5 39.0 - - + +
1397A GLN 2.9 18.4 + - - +
1398A ARG 4.6 0.2 - - - +
1400A LEU* 1.3 77.4 - - - +
1402A GLY* 1.3 67.4 + - - +
1404A GLN 4.3 1.9 - - - +
1406A GLN* 4.0 28.1 + - + +
1555A ARG* 3.6 7.0 - - - +
1561A ASP* 3.3 23.8 - - - +
1562A THR* 5.5 4.1 - - - +
851C ASN* 3.8 10.3 + - - +
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Residues in contact with GLY1402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392A PRO* 5.2 5.4 - - - +
1398A ARG* 3.0 22.7 + - - +
1399A GLN 3.8 5.6 + - - -
1400A LEU 3.7 1.0 - - - -
1401A ARG* 1.3 86.4 - - - +
1403A ALA* 1.3 64.0 + - - -
1404A GLN 3.4 5.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il